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DNA Microarray Data Analysis Workshop - Thailand

The course will be held from August 23 - 27, 2004 (incl.)
Lectures and exercises will take place at Room no. 127, BIOTEC Building, Thailand Science Park, Pathumthani, Thailand

Recommended book: A Biologist's Guide to Analysis of DNA Microarray Data, by professor Steen Knudsen
An introduction to R is available on-line.
Beginner's Guide to UNIX is available on-line.


Course Programme


O Monday, August 23

9.00-9.30
Introduction to the workshop
Hanne Jarmer & H. Bjørn Nielsen, CBS
9:30-10.00
Coffee Break
10.00-11.00
Overview of gene expression and DNA microarray technology.
Different technologies - advantages and disadvantages (Lecture notes)
Hanne Jarmer, CBS
11:00-11.15
Coffee Break
11.15-12.00
Discussion of student's motivations and projects
Hanne Jarmer & H. Bjørn Nielsen, CBS
12.00-13.00
Lunch Break
13.00-14.00
Analysis of the cell cycle (case story) (Lecture notes)
H. Bjørn Nielsen, CBS
14.00-14.15
Coffee Break
14.15-15.30
Short introduction to the statistical language R (Lecture notes) , (Exercise), (The harder exercise)
H. Bjørn Nielsen, CBS
15.30-15.45
Test of the day
15.45->
Preparation of student's data
Hanne Jarmer & H. Bjørn Nielsen, CBS


O Tuesday, August 24

9.00-9.45
Experimental design and setup (Lecture notes)
Hanne Jarmer & H. Bjørn Nielsen, CBS
9:45-10.00
Coffee Break
10.00-11.30
Probe design (incl. exercise) (Lecture notes)
Nielsen.et.al.03.pdf
OligoWiz II
Introduction to regular expressions
H. Bjørn Nielsen, CBS
11.30-12.00
Analysis of probe performance (Lecture notes)
H. Bjørn Nielsen, CBS
12.00-13.00
Lunch Break
13.00-14.00
Sample preparation, hybridization, scanning and image analysis (Lecture notes)
Hanne Jarmer, CBS
14:00-14.15
Coffee Break
14.15-15.15
Arabidopsis transcriptomics (case story) (Petersen.et.al.00.pdf)
H. Bjørn Nielsen, CBS
15.15-15.30
Coffee Break
15.30-15.45
Test of the day


O Wednesday, August 25

9.00-11.00
Normalization (Lecture notes), (Exercise)
H. Bjørn Nielsen, CBS
11:00-11.15
Coffee Break
11.15-12.00
Statistical analysis of microarray data (Lecture notes)
Hanne Jarmer, CBS
12.00-13.00
Lunch Break
13.00-15.00
Statistical analysis of microarray data (Exercise)
Hanne Jarmer, CBS
15.00-15.15
Coffee Break
15.15-16.00
Aspergillus nidulans expression study (case story) (Lecture notes)
H. Bjørn Nielsen, CBS
16.00-16.15
Test of the day


O Thursday, August 26

9.00-10.30
PCA, Clustering and Classification (Lecture notes)
H. Bjørn Nielsen, CBS
10:30-11.00
Coffee Break
11.00-12.00
PCA, Clustering and Classification (Exercise)
H. Bjørn Nielsen, CBS
12.00-13.00
Lunch Break
13.00-13.45
Transcriptome analysis of the TnrA regulon in Bacillus subtilis (case story)
Pathway analysis and regulatory networks (Lecture notes)
Hanne Jarmer, CBS
13:45-14.00
Coffee Break
14.00-15.15
Reverse engineering of regulatory networks (Exercise)
Hanne Jarmer, CBS
15:15-15.30
Coffee Break
15.30-16.00
Promoter analysis, in silico (Lecture notes) , (Demo server)
H. Bjørn Nielsen, CBS
16.15-16.30
Test of the day


O Friday, August 27

9.00-10.00
Lecture and demonstration: CodeLink Bioarrays - A Reliable Microarray-based Assay for Accurate and Precise Expression Profiling and Genotyping Studies
Amersham
10:00-10.15
Coffee Break
10:15-12.30
Automated analysis of array data (Exercise)
Hanne Jarmer, CBS
12.30-13.30
Lunch Break
13.30-14.00
Microarray projects in Thailand - an overview
Supapon Cheevadhanarak, BIOTEC
14.00-16.00
Round table discussion
16.00-16.15
Final discussion and course evaluation
17.00 End of course